It is desirable to determine the isotopic composition, including position-specific and multiple substitutions, of a particular molecule in a user friendly manner which can be applied to different kinds of compounds. Because of the great number of unique isotopic versions of many molecules, any efficient method of analysis should generally be capable of observing the largest fraction of those species that is practical (in light of constraints imposed by time and/or sample size) and interpreting measurements of a sub-set of all possible isotopic species. In particular, it is desirable to balance the need for highly precise measurements of relative abundances of isotopic versions of a molecule—a generally time consuming analysis—against the desire to observe a large number of isotopic versions of each molecular species. Ideally, a measurement algorithm would enable both high precision analyses of a few species, poorer precision analyses of a large number of species, and a model which relates these data types to each other in a self-consistent fashion.